The functions of structure and dynamics in proteins, peptides and metal ion complexes and their relationships to biological recognition and the handling of information

Williams, R. J. P.

doi:10.1007/bf02910424

Cited by 17 publications

(4 citation statements)

References 39 publications

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“…8). This partial constraint on mobility in the loops, as shown by NMR studies of proteins [1], allows induced fitting through the reduced mobility of surface residues but prevents allosteric communication through the protein.…”

Section: The Proteins Best Suited For Catalysis and Pumpsmentioning

confidence: 99%

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The natural selection of the chemical elements

Williams

1997

CMLS, Cell. mol. life sci.

128

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Evolution is treated here in a novel way. DNA or any other code is considered to be conservative and therefore, once life began, it would prevent change. Change was imposed upon the DNA code as a stress resulting in vulnerability to "advantageous" DNA damage and mutation. In this respect it is the stress, the changing environment, that opened up a possibility of evolution once an early life form had optimised itself in primitive circumstances. Here I examine the initial slow-coming-to-terms with the environment of primitive life, and then its evolution as the environment forced the DNA into novel development by introducing chemical elements in new forms. The situation today is no different. Environmental change is hostile to present day life and will lead to further evolution.

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Section: The Proteins Best Suited For Catalysis and Pumpsmentioning

confidence: 99%

“…There are two reasons. First, it was the topic of my Linderstro *m-Lang lecture in 1986 [1]. Second, this year's Linderstro *m-Lang lecturer, Prof. K. Wü thrich will analyse the properties of proteins by NMR using his methods of study which have largely superceded ours.…”

Section: Introductionmentioning

confidence: 99%

The natural selection of the chemical elements

Williams

1997

CMLS, Cell. mol. life sci.

128

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“…The folded protein is a set of four partially helical strands, cross-linked by calcium ions. Other examples are apocytochrome c and metallothionine which only fold around their cofactors ( Table 3) [18].…”

Section: Purtiul Domain Unfoldingmentioning

confidence: 99%

NMR studies of mobility within protein structure

Williams

1989

European Journal of Biochemistry

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NMR studies of dynamics within structure have revealed that a quite new approach to protein structure and its relation to function is necessary. This approach requires the consideration in detail of the following :1. Local movements of groups and small segments to allow fast recognition and fitting. The motion concerns on/off rates as well as binding. The observations affect surface/surface recognition, e.g. of antigen/antibody as well as of substrate and protein.2. Somewhat larger interdomain or N-and C-terminal segments which allow rearrangement. Cases in point are the movement of segments in blood-clotting proteins or in histones.3. Relative motion of helices in hinges. These actions are likely in such enzymes as kinases and P-450 cytochromes.4. Relative motion of helices within domains (relative to other helices or sheets) in mechanical devices (triggers) e.g. in cdlmodulin.5. General motion in random proteins. Examples extend from rubber-like proteins (entropy sensors), some glycoproteins, to proteins carrying peptide hormones to be generated only after hydrolysis.6. Order -+ disorder transitions locally as in osteocalcin and metallothionine. 7. Swinging arm motions associated with special sequences such as (Ala-Pro),. 8. Of great interest is the power of NMR to look at proteins which are relatively large, up to 50 k Da proteins, and to isolate certain zones of interest. This needs careful temperature dependent studies and analysis of separated domains [72] as well as the use of a great variety of pulse sequences [15] and of nuclei other than protons.9. In this article 1 have illustrated the different possibilities using work in my own group. This is done to lessen the burden of extensive review. I fully realise that the range of examples is now large. I would stress though that the production of the necessary technology was the endeavour of several of us within the Oxford Enzyme Group from 1970 to 1985, i.e. from 270-600 MHz Fourier-transform NMR spectroscopy.10. While all of these features have been demonstrated by NMR methods there are parallel developments both using X-ray diffraction methods and theoretical approaches. All these procedures are changing the view of protein structure to one which incorporates dynamics all the way from conventional vibronic/rotational coupling to the disordered motions characteristic of random polymers. It is the understanding of dynamics that leads to an appreciation of function.Correspondence ta R. J. P. Williams, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, EnglandAbbreviations. FUR protein, iron-uptake regulatory protein; NOE, nuclear Overhauser effect; COSY, correlated spectroscopy; NOESY, nuclear Overhauser effect spectroscopy; Gla, y-carboxyglutamate.No&. While this article was being completed, a review was published in the European Journal of Biochemistry [76] which has summarised very effectively some of the problems faced by all users of NMR methods who attempt to describe either structure or dynamics of large flexible...

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“…A candidate that would satisfy this consideration is Zn 2., which is known to exist in DNA-binding proteins (7,65,88), but other trace metals such as Cu 2., Fe 2+, and Mn 2* cannot be eliminated (123).…”

Section: Predicted Characteristics Of the Regulatory Systemmentioning

confidence: 99%

“Light-derepressible” genes are regulated by metal-protein complexes: A hypothesis

Hoober

1988

Carlsberg Res. Commun.

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The hypothesis is presented that genes whose expression is sensitive to light are regulated by metal-protein complexes. This hypothesis is based on induction of a gene for an Mr 21,000 polypeptide in the prokaryote Arthrobacter sp. by photodynamic conditions, chelating agents, or a decrease in pH. It is proposed that these conditions promote dissociation of a regulatory metal-protein complex by photooxidation of the metal-binding site, lowering the concentration of free metal ion, or protonation of amino acid side-chains in the metal-binding site, respectively. Repression of this gene is restored when cells are returned to the dark, metal ions are added in excess of chelating agents or the pH of the medium is returned to neutral. Restoration of repression is inhibited by chloramphenicol and novobiocin, which suggests that this process requires resynthesis of a regulatory protein and reassociation of the complex with DNA. The hypothesis predicts a number of characteristics of the regulatory system, most of which are found among the effects ofphytochrome. The well-documented effects of transition metal ions on the Pfr form ofphytochrome suggest that changes in gene expression in plants mediated by photoisomerisation of this chromoprotein are initiated by a chelating activity of Pfr-

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The functions of structure and dynamics in proteins, peptides and metal ion complexes and their relationships to biological recognition and the handling of information

Cited by 17 publications

References 39 publications

The natural selection of the chemical elements

The natural selection of the chemical elements

NMR studies of mobility within protein structure

“Light-derepressible” genes are regulated by metal-protein complexes: A hypothesis

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